Merge branch 'rsachetto-master'

README.md

@@ -21,7 +21,6 @@ $ ./build.sh
 The binary files will be saved in the ```bin``` folder.
 
 # Running examples
-----
 ```sh
 $ bin/MonoAlg3D -c example_configs/cuboid_ohara.ini 
 ```
@@ -51,11 +50,19 @@ Example file:
 
 This file represents 3 volumes with 100 micrometer of side. The first volume is centered at  at 850,850,950 and the calculated V is -85 mV.
 
+# Contributors:
+
+@rsachetto Rafael Sachetto Oliveira
+
+@bergolho Lucas Arantes Berg
+
+@Rodrigo-Weber-dos-Santos Rodrigo Weber dos Santos
+
+Among others.
+
 # How to cite:
-----
 
 Oliveira RS, Rocha BM, Burgarelli D, Meira Jr W, Constantinides C, dos Santos RW. Performance evaluation of GPU parallelization, space‐time adaptive algorithms, and their combination for simulating cardiac electrophysiology. Int J Numer Meth Biomed Engng. 2018;34:e2913. https://doi.org/10.1002/cnm.2913
 
 # Credits
-----
 [Heart icons created by phatplus - Flaticon](https://www.flaticon.com/free-icons/heart)

build.sh

@@ -239,8 +239,13 @@ if [ -n "$COMPILE_MPI" ]; then
       HDR_FILES=""
       DYNAMIC_DEPS="$DYNAMIC_DEPS $MPI_LIBRARIES"
       EXTRA_LIB_PATH="$EXTRA_LIB_PATH $CUDA_LIBRARY_PATH $MPI_LIBRARY_PATH $LIBRARY_OUTPUT_DIRECTORY"
+
+      if [ -z "$MPI_INCLUDE_PATH" ]; then
+        COMPILE_EXECUTABLE "MonoAlg3D_batch" "$SRC_FILES" "$HDR_FILES" "$STATIC_DEPS" "$DYNAMIC_DEPS" "$CUDA_LIBRARY_PATH $CUDA_MATH_LIBRARY_PATH $EXTRA_LIB_PATH"
+      else
+        COMPILE_EXECUTABLE "MonoAlg3D_batch" "$SRC_FILES" "$HDR_FILES" "$STATIC_DEPS" "$DYNAMIC_DEPS" "$CUDA_LIBRARY_PATH $CUDA_MATH_LIBRARY_PATH $EXTRA_LIB_PATH" "-I$MPI_INCLUDE_PATH"
+      fi
 
-      COMPILE_EXECUTABLE "MonoAlg3D_batch" "$SRC_FILES" "$HDR_FILES" "$STATIC_DEPS" "$DYNAMIC_DEPS" "$CUDA_LIBRARY_PATH $CUDA_MATH_LIBRARY_PATH $EXTRA_LIB_PATH" "-I$MPI_INCLUDE_PATH"
   fi
 
 fi

src/alg/grid/grid.c

@@ -26,6 +26,8 @@ struct grid *new_grid() {
 
     result->purkinje = NULL;
 
+    result->extra_info = NULL;
+
     return result;
 }
 

src/alg/grid/grid.h

@@ -6,7 +6,6 @@
 #define MONOALG3D_GRID_H
 
 #include "../cell/cell.h"
-#include "../../graph/graph.h"
 #include "../grid_purkinje/grid_purkinje.h"
 #include "../../common_types/common_types.h"
 
@@ -39,6 +38,9 @@ struct grid {
 
     struct point_3d start_discretization;
     struct point_3d max_discretization;
+
+    void *extra_info;
+
 };
 
 struct grid* new_grid();